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. 2020 May 15;117(23):12531–12540. doi: 10.1073/pnas.1918619117

Fig. 3.

Fig. 3.

TGA1 is a transcriptional activator that regulates both TFs and N-uptake/assimilation genes in root cells. (A) Workflow of TARGET TF-perturbation assay that can detect the gene targets that TGA1 binds to and regulates in isolated root cells. (B) The TARGET TF-perturbation assay reveals TGA1 directly up-regulates (yellow, 77%) or down-regulates (blue, 23%) the expression of 584 genes in root cells (SI Appendix, Table S4). (C) NLP8 and CIB3 TFs are examples of direct targets transcriptionally activated by TGA1. The expression of NLP8 and CIB3 is affected by TGA1 nuclear import, as assayed by both RNA-seq (steady-state mRNA) and by 4tU affinity capture (de novo mRNA) (green bars). TGA1 binding at these loci was captured by ChIP-seq (red bars). (D) TGA1 transcriptional subnetwork in root cells, where nodes represent genes and edges represent regulatory interactions detected by our assay. TGA1 directly or indirectly—through intermediate TFs (triangles)—regulate the expression genes involved in N uptake/metabolism (circles).